User: Burnedthumb

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Burnedthumb90
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Posts by Burnedthumb

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Recommendations about phylogenetic analysis tools for RFLP/AFLP/RAPD data
... You can make the plot as big as you want, however at that size it will be unreadable and won't get any information out it. You may want to filter the data a little bit first for the most interesting samples. Or you can cut[1] the tree at a specific height and plot those sub trees separately. [1] h ...
written 6 months ago by Burnedthumb90
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Comment: C: Recommendations about phylogenetic analysis tools for RFLP/AFLP/RAPD data
... R itself will handle data up to a couple of gigabytes just fine. However, if you want to plot hundreds or thousands of samples the image gets unreadable. What you could do is instead of regular plotting, writing the dendrogram to a file like this: ## Plot the data to image with 1000 pixels widt ...
written 6 months ago by Burnedthumb90
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Answer: A: Recommendations about phylogenetic analysis tools for RFLP/AFLP/RAPD data
... You could use R in combination with the proxy package: Given your dataset as a tab delimited dataset "dataset.txt": SNP St1 St2 St3 St4 St5 St6 1284995 0 0 0 1 0 0 1285001 1 1 1 0 1 1 1285017 0 0 0 0 0 0 1285034 0 0 1 0 0 0 1285040 0 1 0 0 0 0 1285070 0 0 0 0 1 1 Then ...
written 6 months ago by Burnedthumb90
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Answer: A: CLC GW vs. tophat2
... Both Tophat2 and STAR are splice aware aligners. If I recall correctly, the default alignment program of CLC bio is not. Maybe you can verify which of the aligners they used, maybe they used the RNAseq pipeline which (should) work differently. A couple of months back I did some tests with CLC bio v ...
written 2.3 years ago by Burnedthumb90
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Answer: A: Aligning MiSeq targeted amplicons (ultra-deep sequencing)
... I have seen this before, and I don't think this is something to worry about. Your data analysis method looks fine. Check the basequality of those of 'weird' bases, they are probably very low. If you run a SNP caller on your bam file, those artifacts will not interfere as most SNP callers take in acc ...
written 3.0 years ago by Burnedthumb90
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Answer: A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
... Instead of using bioperl, you can also specify which field you want using the "-outfmt" tag. Like this: blastn -db your_database -query your_query.fasta -outfmt "6 qseqid sseqid score bitscore evalue" >> blastout.txt ...
written 6.2 years ago by Burnedthumb90
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Comment: C: Amplicon Sequencing
... I will give this one a try. Thank you very much! ...
written 6.5 years ago by Burnedthumb90
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Amplicon Sequencing
... Hi, I am looking for an alignment tool that is good at aligning a lot of small amplicon sequences to small reference sequences. I have tried BWA and Bowtie, (and BLAST with a makeshift Perl parser behind it) but can someone point me to another good alignment program for this kind of job? Kind reg ...
bowtie bwa sequencing written 6.5 years ago by Burnedthumb90 • updated 6.5 years ago by Josh Herr5.5k

Latest awards to Burnedthumb

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Recommendations about phylogenetic analysis tools for RFLP/AFLP/RAPD data
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Amplicon Sequencing

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